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Sebastián Ayala-Ruano
I am a focused and motivated young researcher that has worked in Bioinformatics for four years at different laboratories. Phylogenetics and Structural Bioinformatics have been the main topics of this research experience. However, my current interests are devoted to Network Science, Complex Systems, and Machine Learning to understand different biological phenomena.
I am involved in various initiatives to empower Bioinformatics in Ecuador and Latin America.
Education
B.Eng., Biotechnology
Universidad San Francisco de Quito (USFQ)
Quito, Ecuador
2020 - 2015
- Minor: Systems engineering.
- GPA: 3.77/4 (Magna Cum Laude)
- Thesis: Computational study of the structural changes of two Cereblon protein mutations using Molecular Dynamics and Quantum Mechanics.
- Advisor: Miguel Angel Méndez Silva
Research Experience
Applied Signal Processing and Machine Learning Research Group - USFQ
Research Assistant
Quito, Ecuador
Current - 2021
- Performing an unsupervised learning approach based on network science and similarity searching to explore the chemical space of antiparasitic peptides, and discover new potential drugs.
- Advisors: Yovani Marrero-Ponce, Noel Pérez Pérez
Computational and Theoretical Chemistry Group - USFQ
Undergraduate Researcher
Quito, Ecuador
2020 - 2017
- Identified binding specificity between repressor proteins and a transcriptional factor associated with the Jasmonic Acid pathway in Arabidopsis thaliana through Molecular Dynamics simulations and Machine Learning algorithms.
- Proposed molecular mimicry between Zika envelope protein and human neuronal proteins through structural similarity predictors, Molecular Dynamics, and Protein-Protein Interaction Networks.
- Advisor: Miguel Angel Méndez Silva
Bio-Chemoinformatics Group - Universidad de Las Américas
Research Intern
Quito, Ecuador
2020 - 2018
- Understood the impact of horizontal gene transfer in the genome of Streptomyces clavuligerus using Phylogeny, RNAseq data, and other bioinformatics tools.
- Performed genomic comparative study of genes related to lignin degradation through Protein-protein Interaction Networks.
- Advisor: Vinicio Armijos
Tumor Metabolism and Therapeutic Oncology Laboratory - Gwangju Institute of Science and Technology
Research Intern
Gwangju, South Korea
2019
- Performed a computational study of a missense mutation from Cereblon protein using Molecular Dynamics and Quantum Mechanics simulations, and other bioinformatics tools.
- Advisors: Miguel Angel Méndez Silva, Steve K. Cho
Teaching Experience
Linux and Bash/AWK scripting Boot Camp
Virtual event
2021
- Co-organizer and co-instructor.
- Designed and taught most of the course material, which was held for five weeks.
- Covered the basics of Linux, terminal usage, text and file processing command line tools, Bash/AWK scripting with applications in Bioinformatics, and Git/GitHub.
Undergraduate Teaching Assistant
Learning Center - USFQ
Virtual events
2020
- Provided online mentorship of Biotechnology, Mathematics, and Systems Engineering subjects to undergraduate students that needed help.
Undergraduate Teaching Assistant
General Biology Laboratory - USFQ
Quito, Ecuador
2018 - 2016
- Graded reports, tests, and other homework from the course.
- Provided feedback and guidance to undergraduate students in topics of the course.
- Helped to design experiments for lectures.
Publications
4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID19 times
Editorial journal article
N/A
2020
- Castillo-Vilcahuaman, C., Valdivia C., Osorio-Mogollón C., Silva-Andrade, C., Puche, R., Ayala‐Ruano, S., Cuesta-Astroz, Y., Parra, G. F1000Research (2020). doi: 10.12688/f1000research.28330.1.
The molecular basis of JAZ-MYC coupling, a protein-protein interface essential for plant response to stressors
Peer reviewed journal article
N/A
2020
- Oña-Chuquimarca, S., Ayala-Ruano, S., Goossens, Pauwels, L., Goossens, A., Leon-Reyes, A., & Méndez, M. A. Frontiers in Plant Science (2020). doi: 10.3389/fpls.2020.01139.
- This article was chosen to feature in the Frontiers in Plant Science 2020 highlights e-book collection. doi: 10.3389/978-2-88966-723-9
A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications
Peer reviewed journal article
N/A
2019
- Ayala‐Ruano, S., Santander‐Gordón, D., Tejera, E., Perez‐Castillo, Y., & Armijos-Jaramillo, V. Ecology and Evolution (2019). doi: 10.1002/ece3.4924.
Uncovering JAZ-MYC biochemical and structural interactions
Peer-reviewed Conference Proceeding
N/A
2019
- Oña-Chuquimarca, S., Ayala-Ruano, S., Gallardo, S., & Méndez, M. A. _ International work-conference on Bioinformatics and biomedical engineering (IWBBIO 2019)_ (2019) ISBN: 978-8417293-94-9
Conference presentations
Modeling of protein-protein interaction and search for key residues by machine learning of the JAZ-MYC3 complex of Arabidopsis thaliana
5th RSG-Argentine Symposium of Young Researchers in Bioinformatics
Virtual event
2020
- Oral presentation
- Authored with Samara Oña-Chuquimarca and Miguel Ángel Méndez.
In silico detection of horizontal gene transfer in Streptomyces clavuligerus
International Society for Computational Biology Student Council Webinar series
Virtual event
2020
- Oral presentation
- Authored with Vinicio Armijos.
In silico detection of an antimicrobial peptide (AMP) transferred horizontally from arthropods to bacteria
2nd RSG-Colombia Symposium of young researchers in Bioinformatics
Ibagué, Colombia
2019
- Oral presentation
- Authored with Vinicio Armijos.
Modeling of Protein-protein interaction and search for key residues by machine learning of a protein complex in the jasmonic acid route in Arabidopsis thaliana
XLIII National Biology Conference
Urcuquí, Ecuador
2019
- Poster presentation
- Authored with Samara Oña-Chuquimarca and Miguel Ángel Méndez.
Structural changes due to a mutation in Cereblon might be a cause for intellectual disability
Global Intern Program at Gwangju Institute of Science and Technology
Gwangju, South Korea
2019
- Poster presentation
- Authored with Miguel Ángel Méndez, Francisco Yanqui-Rivera, and Steve K. Cho
Uncovering JAZ-MYC biochemical and structural interactions
7th International work-conference on Bioinformatics and Biomedical Engineering
Granada, Spain
2019
- Poster presentation
- Authored with Samara Oña-Chuquimarca and Miguel Ángel Méndez.
Characterization of the proteome of the babaco mosaic virus (BMV)
VI Ecuadorian Congress of Information Technologies
Riobamba, Ecuador
2018
- Oral presentation
- Authored with Miguel Ángel Méndez.
Honors and Awards
Innovation challenge For more data of labor informality award
Datalat, PNUD Ecuador, UN Women Ecuador, and the International Labour Organization
Virtual event
2021
- This competition searched for a technological solution to collect labor informality data in Ecuador. There were 39 proposals from 80 interdisciplinary teams. This blog has a detailed explanation of the challenge.
- The economic award of all stages of the competition was $ 4.300
Chancellor’s Honor List
Universidad San Francisco de Quito
Quito, Ecuador
2020 - 2016
- This award recognizes students who have a GPA of 3.7/4 or higher.
Third HPC Summer School Colombia: Bio and Data Science scholarship
Virtual event
2020
- The scholarship covered registration expenses for the event.
Saturdays.AI Quito 2020 scholarship
Virtual event
2020
- The scholarship covered registration expenses for the Saturdays.AI Quito 2021.
2nd RSG-Colombia Symposium of young researchers in Bioinformatics travel award
RSG Colombia
Ibagué, Colombia
2019
- This award covered the travel expenses to attend the event.
Global Intern Program
Gwangju Institute of Science and Technology
Gwangju, South Korea
2019
- The GIP awarded students with accommodation and a monthly stipend to cover living expenses for eight weeks. During this time, we were involved in a research project and received valuable training and mentoring.
Leadership and Service
Regional Student Group Ecuador
International Society for Computational Biology Student Council
Quito, Ecuador
Current - 2020
- Co-founder and current president of the RSG Ecuador
- This group aims to create a long-lasting community of students, professors, and researchers residing in Ecuador, capable of learning, teaching, and using technologies related to Bioinformatics.
17th Student Council Symposium
International Society for Computational Biology Student Council
Virtual event
2021
- I was the fellowship committee chair and contributed to other organization tasks.
4th ISCB Latin American Student Council Symposium
International Society for Computational Biology Student Council
Virtual event
2020
- I contributed to the program and fellowships committees.
Saturdays.AI Quito 2020 scholarship
Virtual event
2020
- I led the project presented for my group at this event.
- Our project was an information extraction tool that found relevant scientific articles related to questions about COVID-19. For this task, we applied some Natural Language Processing algorithms. The code of this project is available in this GitHub repository.
Biotechnology club
Universidad San Francisco de Quito
Quito, Ecuador
2019 - 2018
- This club aimed to develop projects in base of the knowledge acquired throughout our career, learn about certain topics not covered in our courses, and communicate science topics to other students and the overall community.